I recently using Arduino IDE with my custom, variation of Due's board. Now im trying to use Atmel Studio 7 Visual Micro with "no IDE" option, but i don't know where can I add or edit configuration files? Recently in Arduino IDE i was copied folder arduino_due_x located at:

C:\Users\username\AppData\Local\Arduino15\packages\arduino\hardware\sam\1.6.11\variants\arduino_due_x
to
C:\Users\username\AppData\Local\Arduino15\packages\arduino\hardware\sam\1.6.11\variants\arduino_due_x_modified

after some changes inlinker scripts I was added new board named "arduino_due_x_modified" at the end of file boards.txt:
C:\Users\username\AppData\Local\Arduino15\packages\arduino\hardware\sam\1.6.11\boards.txt

after that in Arduino IDE appears new board "arduino_due_x_modified" It is possible to do that way using "Visual Micro (No IDE)" ?

1)
Visual Micro should be using the same system. Did you restart the ide or click Rescan on the Micro explorer?

2)
If you have the arduino ide installed then there is no point in using the (No IDE) option. Please configure the Arduino 1.6/1.8 IDE option to avoid confusion

The mentioned locations is from my another machine, where I'm using arduino IDE from long time, but after I tested AS7 with Visual Micro i don't want to use it any more. So I want to break up with arduino IDE completly,but im using customized bootloader, that needs modified linker, this is the reason for additional custom board. But ok if there is no option for add my old configuration I will install Arduino IDE and do rescan.

It should work the same if you have edited arduino15\packages

You must make sure you have given you custom board a unique id

for example if normally you see atmega2560= change that to MyAtmega2560=

I you want to use custom avr boards this is best achiever with the older arduino way of doing things in documents\arduino\hardware